Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations | Zendy

Hongyi Zhou | Zendy; Chi Zhang | Zendy; S. Liu | Zendy; Yaoqi Zhou | Zendy

Open Access

Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations

Author(s) -

Hongyi Zhou,

Chi Zhang,

S. Liu,

Yaoqi Zhou

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki360

Subject(s) - biology , transmembrane domain , protein structure prediction , protein tertiary structure , web server , protein folding , computational biology , protein structure , sequence alignment , folding (dsp implementation) , protein secondary structure , protein engineering , transmembrane protein , sequence analysis , protein domain , protein design , peptide sequence , hidden markov model , multiple sequence alignment , loop modeling , biochemistry , amino acid , computer science , dna , artificial intelligence , gene , receptor , electrical engineering , engineering , the internet , world wide web , enzyme

We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMM(TMHP) and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMM(TMHP)) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile-profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP3); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity of protein-protein/peptide/DNA complexes (DCOMPLEX & DDNA); TCD, a program for protein-folding rate and transition-state analysis of small globular proteins; and DOGMA, a web-server that allows comparative analysis of domain combinations between plant and other 55 organisms. These servers provide tools for prediction and/or analysis of proteins on the secondary structure, tertiary structure and interaction levels, respectively.

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